Trends in KEEN QUAD Data

What species are in the quad data?

SP_CODE	COMMON.NAME	SPECIES
AGCL	Shotgun Kelp	Agarum clathratum
AGJ	Juv. Shotgun Kelp	Agarum clathratum
CAIS	Atlantic Rock Crab	Cancer irroratus
CEBO	Northern cerianthid	Pachycerianthus borealis
COPE	Sea Potato	Colpomenia peregrina
DEAC	Sour or Stink Weed	Desmarestia aculeata
ECPA	common sand dollar	Echinarachnius parma
HATO	Hairy Shoelace	Halosiphon tomentosus
HESA	Blood Star	Henricia sanguinolenta
HESAS	Blood Star	Henricia sanguinolenta
HOAM	American lobster	Homarus americanus
HOAS	American lobster	Homarus americanus
MYSP	Sculpin	Myoxocephalus
PHGU	Rock gunnel	Pholis gunnellus
SADE	Oarweed	Saccorhiza dermatodea
SDL	Green Sea Urchin	Strongylocentrotus droebachiensis
SDS	Green Sea Urchin	Strongylocentrotus droebachiensis
SL	Sugar Kelp	Saccharina latissima
SLJ	Juvenile Sugar Kelp	Saccharina latissima

Let’s Plot Trends

Here are some functions we’ll apply to each species. I’ll then fit mixed models with all of them using

COUNT ~ YEAR * SITE + (1|TRANSECT)

with a gaussian error. Note, it’s count, so, I could use Poisson, but, that needs to be way more tuned to each model - this should be fine for a first cut?

Here’s how we’ll do it:

tseries_plot <- function(adf){
  
  ggplot(adf,
         aes(y = COUNT, x = YEAR,
             color = TRANSECT)) +
    stat_summary(fun.data = mean_se) +
    stat_summary(fun.data = mean_se, geom = "line") +
    facet_wrap(~SITE, nrow = 2) +
    labs(color = "Transect", 
         y = "Count per sq m ± SE",  x = "Year",
         title = adf$SPECIES[1])
}

tseries_fun <- function(adf){
  glmmTMB(COUNT ~ YEAR * SITE + (1|TRANSECT),
               data = adf,
               family = gaussian)
  
}

generate_output <- function(adf){
  cat(paste0("## ", adf$SP_CODE[1], " ", adf$SPECIES[1], "  \n<br>"))
  
  tseries_plot(adf) %>% print()
  
  # tseries_fun(adf) %>% 
  #   car::Anova(test.statistic  = "Chisq") %>% 
  #   tidy() %>%
  #   knitr::kable("html", digits = 3) %>% 
  #   kableExtra::kable_styling() %>%
  #   print
  # 
  cat("\n\n")
}

Now let’s purrr::walk() through the whole shebang.

walk(split(quad, quad$SP_CODE), generate_output)

AGCL Agarum clathratum

AGJ Agarum clathratum

CAIS Cancer irroratus

CEBO Pachycerianthus borealis

COPE Colpomenia peregrina

DEAC Desmarestia aculeata

ECPA Echinarachnius parma

HATO Halosiphon tomentosus

HESA Henricia sanguinolenta

HESAS Henricia sanguinolenta

HOAM Homarus americanus

HOAS Homarus americanus

MYSP Myoxocephalus

PHGU Pholis gunnellus

SADE Saccorhiza dermatodea

SDL Strongylocentrotus droebachiensis

SDS Strongylocentrotus droebachiensis

SL Saccharina latissima

SLJ Saccharina latissima